+Open data
-Basic information
Entry | Database: PDB / ID: 6j5s | |||||||||
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Title | Crystal structure of human HINT1 mutant complexing with AP5A | |||||||||
Components | Histidine triad nucleotide-binding protein 1 | |||||||||
Keywords | HYDROLASE / NUCLEOTIDE BINDING / REGULATION OF TRANSCRIPTION / SIGNAL TRANSDUCTION | |||||||||
Function / homology | Function and homology information purine ribonucleotide catabolic process / adenylylsulfatase activity / Hydrolases; Acting on phosphorus-nitrogen bonds / adenosine 5'-monophosphoramidase activity / deSUMOylase activity / protein desumoylation / sulfur compound metabolic process / histone deacetylase complex / intrinsic apoptotic signaling pathway by p53 class mediator / positive regulation of calcium-mediated signaling ...purine ribonucleotide catabolic process / adenylylsulfatase activity / Hydrolases; Acting on phosphorus-nitrogen bonds / adenosine 5'-monophosphoramidase activity / deSUMOylase activity / protein desumoylation / sulfur compound metabolic process / histone deacetylase complex / intrinsic apoptotic signaling pathway by p53 class mediator / positive regulation of calcium-mediated signaling / protein kinase C binding / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / cytoskeleton / hydrolase activity / nucleotide binding / regulation of DNA-templated transcription / signal transduction / proteolysis / extracellular exosome / nucleoplasm / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.02 Å | |||||||||
Authors | Wang, J. / Fang, P. / Guo, M. | |||||||||
Funding support | China, 2items
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Citation | Journal: Nat Commun / Year: 2019 Title: Second messenger Ap4A polymerizes target protein HINT1 to transduce signals in Fc epsilon RI-activated mast cells. Authors: Yu, J. / Liu, Z. / Liang, Y. / Luo, F. / Zhang, J. / Tian, C. / Motzik, A. / Zheng, M. / Kang, J. / Zhong, G. / Liu, C. / Fang, P. / Guo, M. / Razin, E. / Wang, J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6j5s.cif.gz | 131.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6j5s.ent.gz | 100.8 KB | Display | PDB format |
PDBx/mmJSON format | 6j5s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6j5s_validation.pdf.gz | 783.8 KB | Display | wwPDB validaton report |
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Full document | 6j5s_full_validation.pdf.gz | 787.1 KB | Display | |
Data in XML | 6j5s_validation.xml.gz | 17.8 KB | Display | |
Data in CIF | 6j5s_validation.cif.gz | 26.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j5/6j5s ftp://data.pdbj.org/pub/pdb/validation_reports/j5/6j5s | HTTPS FTP |
-Related structure data
Related structure data | 5ed3C 5ed6C 6j53C 6j58C 6j5zC 6j64C 6j65C 4eqeS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 13957.096 Da / Num. of mol.: 2 / Mutation: H114A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HINT1, HINT, PKCI1, PRKCNH1 / Production host: Escherichia coli (E. coli) / References: UniProt: P49773, Hydrolases #2: Chemical | ChemComp-AP5 / | #3: Chemical | ChemComp-ESA / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.09 Å3/Da / Density % sol: 41.25 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: HEPES pH 7.5, PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.97946 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 27, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 1.02→50 Å / Num. obs: 115657 / % possible obs: 98.7 % / Redundancy: 4 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 28.9 |
Reflection shell | Resolution: 1.02→1.04 Å / Rmerge(I) obs: 0.456 / Num. unique obs: 3824 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4EQE Resolution: 1.02→32.421 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 0.12 / Phase error: 17.18 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 90.34 Å2 / Biso mean: 13.8294 Å2 / Biso min: 4.87 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.02→32.421 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10
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Refinement TLS params. | Method: refined / Origin x: 13.0595 Å / Origin y: 1.1721 Å / Origin z: 16.0833 Å
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Refinement TLS group | Selection details: all |